Epigenetic Target Information

General Information of the Epigenetic Target (ID: EPITAR00555)

Target Name	Cadherin-4 (CDH4)
Synonyms	Retinal cadherin; R-CAD; R-cadherin Click to Show/Hide
Gene Name	CDH4
Sequence	MTAGAGVLLLLLSLSGALRAHNEDLTTRETCKAGFSEDDYTALISQNILEGEKLLQVKFSSCVGTKGTQYETNSMDFKVGADGTVFATRELQVPSEQVAFTVTAWDSQTAEKWDAVVRLLVAQTSSPHSGHKPQKGKKVVALDPSPPPKDTLLPWPQHQNANGLRRRKRDWVIPPINVPENSRGPFPQQLVRIRSDKDNDIPIRYSITGVGADQPPMEVFSIDSMSGRMYVTRPMDREEHASYHLRAHAVDMNGNKVENPIDLYIYVIDMNDNRPEFINQVYNGSVDEGSKPGTYVMTVTANDADDSTTANGMVRYRIVTQTPQSPSQNMFTINSETGDIVTVAAGLDREKVQQYTVIVQATDMEGNLNYGLSNTATAIITVTDVNDNPPEFTASTFAGEVPENRVETVVANLTVMDRDQPHSPNWNAVYRIISGDPSGHFSVRTDPVTNEGMVTVVKAVDYELNRAFMLTVMVSNQAPLASGIQMSFQSTAGVTISIMDINEAPYFPSNHKLIRLEEGVPPGTVLTTFSAVDPDRFMQQAVRYSKLSDPASWLHINATNGQITTAAVLDRESLYTKNNVYEATFLAADNGIPPASGTGTLQIYLIDINDNAPELLPKEAQICEKPNLNAINITAADADVDPNIGPYVFELPFVPAAVRKNWTITRLNGDYAQLSLRILYLEAGMYDVPIIVTDSGNPPLSNTSIIKVKVCPCDDNGDCTTIGAVAAAGLGTGAIVAILICILILLTMVLLFVMWMKRREKERHTKQLLIDPEDDVRDNILKYDEEGGGEEDQDYDLSQLQQPEAMGHVPSKAPGVRRVDERPVGAEPQYPIRPMVPHPGDIGDFINEGLRAADNDPTAPPYDSLLVFDYEGSGSTAGSVSSLNSSSSGDQDYDYLNDWGPRFKKLADMYGGGEED Click to Show/Hide
Function	Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. May play an important role in retinal development. Click to Show/Hide
Gene ID	1002
HGNC ID	HGNC:1763
Ensembl Gene ID	ENSG00000179242
KEGG ID	hsa:1002
Chromosomal Location	20q13.33

RNA Modification Sequencing Data Associated with the Target (ID: EPITAR00555)

Cadherin-4 (CDH4)

Adenosine-to-Inosine editing (A-to-I)

In total 5 m6A sequence/site(s) in this target gene
mod ID: A2ISITE010796		Click to Show/Hide the Full List
mod site	chr20:61305965-61305966:+		[1]
Sequence	TTTGTAAGCCTTCTGCCAATAGCACCACTTCCGTTGACCTT
Transcript ID List	ENST00000614565.5
External Link	RMBase: RNA-editing_site_88594
mod ID: A2ISITE010797		Click to Show/Hide the Full List
mod site	chr20:61614070-61614071:+		[1]
Sequence	GTGGAATGAGAAATTGACTTAGTCTTTGTCCAGGTTCCTGG
Transcript ID List	rmsk_5169241; ENST00000614565.5; ENST00000611855.4; ENST00000543233.2
External Link	RMBase: RNA-editing_site_88595
mod ID: A2ISITE010798		Click to Show/Hide the Full List
mod site	chr20:61891093-61891094:+		[1]
Sequence	AGAGGGACAACACACCCGCAAGCACAGAGGGGCAGGGATAG
Transcript ID List	ENST00000543233.2; ENST00000611855.4; ENST00000614565.5
External Link	RMBase: RNA-editing_site_88596
mod ID: A2ISITE010799		Click to Show/Hide the Full List
mod site	chr20:61891266-61891267:+		[1]
Sequence	CTCAGCAACTGGTCACGGCTATGTGGTCAGCAGAACACAGT
Transcript ID List	ENST00000614565.5; ENST00000543233.2; ENST00000611855.4
External Link	RMBase: RNA-editing_site_88597
mod ID: A2ISITE010800		Click to Show/Hide the Full List
mod site	chr20:61940464-61940465:+		[2]
Sequence	ATTTTGTACCAAAAAAAAAAAGGAAAAAAAAAGGGAAGAGA
Transcript ID List	ENST00000614565.5; rmsk_5169619
External Link	RMBase: RNA-editing_site_88598

N6-methyladenosine (m6A)

In total 20 m6A sequence/site(s) in this target gene
mod ID: M6ASITE054129		Click to Show/Hide the Full List
mod site	chr20:61252323-61252324:+		[3]
Sequence	GGGAACGCGCCGCCGGCCGGACTTGGCCTGGCTCCCGGAGC
Motif Score	4.065041667
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000614565.5
External Link	RMBase: m6A_site_539378
mod ID: M6ASITE054130		Click to Show/Hide the Full List
mod site	chr20:61743594-61743595:+		[3]
Sequence	GCTGTGTGGGGACCAAGGGGACACAATATGAGACCAACAGC
Motif Score	3.643047619
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000611855.4; ENST00000614565.5; ENST00000543233.2
External Link	RMBase: m6A_site_539382
mod ID: M6ASITE054131		Click to Show/Hide the Full List
mod site	chr20:61743606-61743607:+		[3]
Sequence	CCAAGGGGACACAATATGAGACCAACAGCATGGACTTCAAA
Motif Score	2.876744048
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000543233.2; ENST00000611855.4; ENST00000614565.5
External Link	RMBase: m6A_site_539383
mod ID: M6ASITE054132		Click to Show/Hide the Full List
mod site	chr20:61743619-61743620:+		[3]
Sequence	ATATGAGACCAACAGCATGGACTTCAAAGTTGGGGCAGATG
Motif Score	4.065041667
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000611855.4; ENST00000614565.5; ENST00000543233.2
External Link	RMBase: m6A_site_539384
mod ID: M6ASITE054133		Click to Show/Hide the Full List
mod site	chr20:61743642-61743643:+		[3]
Sequence	TCAAAGTTGGGGCAGATGGGACAGTCTTCGCCACCCGGGAG
Motif Score	3.643047619
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000614565.5; ENST00000611855.4; ENST00000543233.2
External Link	RMBase: m6A_site_539385
mod ID: M6ASITE054134		Click to Show/Hide the Full List
mod site	chr20:61743709-61743710:+		[3]
Sequence	GTTCACGGTGACTGCATGGGACAGCCAGACAGCAGAGAAAT
Motif Score	3.643047619
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000611855.4; ENST00000614565.5; ENST00000543233.2
External Link	RMBase: m6A_site_539386
mod ID: M6ASITE054135		Click to Show/Hide the Full List
mod site	chr20:61743717-61743718:+		[3]
Sequence	TGACTGCATGGGACAGCCAGACAGCAGAGAAATGGGACGCC
Motif Score	2.897386905
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000543233.2; ENST00000611855.4; ENST00000614565.5
External Link	RMBase: m6A_site_539387
mod ID: M6ASITE054136		Click to Show/Hide the Full List
mod site	chr20:61743762-61743763:+		[3]
Sequence	TGCGGTTGCTGGTGGCCCAGACCTCGTCCCCGCACTCTGGA
Motif Score	2.876744048
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000543233.2; ENST00000614565.5; ENST00000611855.4
External Link	RMBase: m6A_site_539388
mod ID: M6ASITE054137		Click to Show/Hide the Full List
mod site	chr20:61743782-61743783:+		[3]
Sequence	ACCTCGTCCCCGCACTCTGGACACAAGGTAAGGTGTGACCG
Motif Score	3.643047619
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000611855.4; ENST00000543233.2; ENST00000614565.5
External Link	RMBase: m6A_site_539389
mod ID: M6ASITE054138		Click to Show/Hide the Full List
mod site	chr20:61773033-61773034:+		[3]
Sequence	AAAGAAGGTCGTGGCTCTGGACCCCTCTCCGCCTCCGAAGG
Motif Score	3.622404762
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000543233.2; ENST00000611855.4; ENST00000614565.5
External Link	RMBase: m6A_site_539390
mod ID: M6ASITE054139		Click to Show/Hide the Full List
mod site	chr20:61773054-61773055:+		[3]
Sequence	CCCCTCTCCGCCTCCGAAGGACACCCTGCTGCCGTGGCCCC
Motif Score	3.643047619
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000543233.2; ENST00000611855.4; ENST00000614565.5
External Link	RMBase: m6A_site_539391
mod ID: M6ASITE054140		Click to Show/Hide the Full List
mod site	chr20:61773114-61773115:+		[3]
Sequence	GCTGAGGCGGCGCAAACGGGACTGGGTCATCCCGCCCATCA
Motif Score	4.065041667
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000611855.4; ENST00000543233.2; ENST00000614565.5
External Link	RMBase: m6A_site_539392
mod ID: M6ASITE054141		Click to Show/Hide the Full List
mod site	chr20:61773147-61773148:+		[3]
Sequence	GCCCATCAACGTGCCCGAGAACTCGCGCGGGCCCTTCCCGC
Motif Score	3.373380952
Cell/Tissue List	Jurkat
Seq Type List	m6A-seq
Transcript ID List	ENST00000611855.4; ENST00000543233.2; ENST00000614565.5
External Link	RMBase: m6A_site_539393
mod ID: M6ASITE054142		Click to Show/Hide the Full List
mod site	chr20:61938175-61938176:+		[4]
Sequence	GTGCCTCTCCTCTCCTATGGACCCTCGTCGGGGGCAGGCAG
Motif Score	3.622404762
Cell/Tissue List	HEK293A-TOA
Seq Type List	m6A-seq
Transcript ID List	ENST00000614565.5
External Link	RMBase: m6A_site_539394
mod ID: M6ASITE054143		Click to Show/Hide the Full List
mod site	chr20:61938209-61938210:+		[4]
Sequence	CAGGCAGCGGCCGGGTCCAAACTTGCTGCTGTCCTCGAGGC
Motif Score	2.627720238
Cell/Tissue List	HEK293A-TOA
Seq Type List	m6A-seq
Transcript ID List	ENST00000614565.5
External Link	RMBase: m6A_site_539395
mod ID: M6ASITE054144		Click to Show/Hide the Full List
mod site	chr20:61938269-61938270:+		[4]
Sequence	GCTGGGTTGACTCAAGCCAGACAGGGGGAAGGAATTGGTTC
Motif Score	2.897386905
Cell/Tissue List	HEK293A-TOA
Seq Type List	m6A-seq
Transcript ID List	ENST00000614565.5
External Link	RMBase: m6A_site_539396
mod ID: M6ASITE054145		Click to Show/Hide the Full List
mod site	chr20:61938527-61938528:+		[5]
Sequence	AAGGAGGTGAGGTACCAGGGACCCTGGGCAGGACCTGGTGT
Motif Score	3.622404762
Cell/Tissue List	HeLa
Seq Type List	m6A-seq
Transcript ID List	ENST00000614565.5
External Link	RMBase: m6A_site_539397
mod ID: M6ASITE054146		Click to Show/Hide the Full List
mod site	chr20:61938539-61938540:+		[5]
Sequence	TACCAGGGACCCTGGGCAGGACCTGGTGTCGGGCAGGGCGG
Motif Score	3.622404762
Cell/Tissue List	HeLa
Seq Type List	m6A-seq
Transcript ID List	ENST00000614565.5
External Link	RMBase: m6A_site_539398
mod ID: M6ASITE054147		Click to Show/Hide the Full List
mod site	chr20:61938578-61938579:+		[5]
Sequence	GGTGCCAGCACTGGGGAAGGACAGGGAGCCCTCCCGGAGCC
Motif Score	3.643047619
Cell/Tissue List	HeLa
Seq Type List	m6A-seq
Transcript ID List	ENST00000614565.5
External Link	RMBase: m6A_site_539399
mod ID: M6ASITE094721		Click to Show/Hide the Full List
mod site	KI270869.1:51827-51828:+		[6]
Sequence	GTGCCTCTCCTCTCCTATGGACCCTCGTCGGGGGCAGGCAG
Motif Score	3.622404762
Cell/Tissue List	MSC
Seq Type List	MeRIP-seq
Transcript ID List	ENST00000625686.1
External Link	RMBase: m6A_site_881422

Ref 1	RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res. 2014 Jan;42(Database issue):D109-13. doi: 10.1093/nar/gkt996. Epub 2013 Oct 25.
Ref 2	Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Res. 2012 Jan;22(1):142-50. doi: 10.1101/gr.124107.111. Epub 2011 Sep 29.
Ref 3	N(6)-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression. Elife. 2016 Jul 2;5:e15528. doi: 10.7554/eLife.15528.
Ref 4	The U6 snRNA m(6)A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention. Cell. 2017 May 18;169(5):824-835.e14. doi: 10.1016/j.cell.2017.05.003.
Ref 5	VIRMA mediates preferential m(6)A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. Cell Discov. 2018 Feb 27;4:10. doi: 10.1038/s41421-018-0019-0. eCollection 2018.
Ref 6	Viral and cellular N(6)-methyladenosine and N(6),2'-O-dimethyladenosine epitranscriptomes in the KSHV life cycle. Nat Microbiol. 2018 Jan;3(1):108-120. doi: 10.1038/s41564-017-0056-8. Epub 2017 Nov 6.

Epigenetic Target Information

Cite M6AREG

Correspondence

Prof. Feng ZHU

Prof. Shuiping Liu

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